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- PDB-5dc4: CRYSTAL STRUCTURE OF MONOBODY AS25/ABL1 SH2 DOMAIN COMPLEX, CRYSTAL A -

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Basic information

Entry
Database: PDB / ID: 5dc4
TitleCRYSTAL STRUCTURE OF MONOBODY AS25/ABL1 SH2 DOMAIN COMPLEX, CRYSTAL A
Components
  • AS25 monobody
  • Tyrosine-protein kinase ABL1
KeywordsPROTEIN BINDING / ENGINEERED BINDING PROTEIN / ANTIBODY MIMIC / PROTEIN-PROTEIN COMPLEX / SH2 DOMAIN / TYROSINE-PROTEIN KINASE
Function / homology
Function and homology information


negative regulation of monocyte activation / : / positive regulation of actin filament binding / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / Fibronectin matrix formation / podocyte apoptotic process ...negative regulation of monocyte activation / : / positive regulation of actin filament binding / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / Fibronectin matrix formation / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / Extracellular matrix organization / response to epinephrine / transitional one stage B cell differentiation / positive regulation of substrate-dependent cell migration, cell attachment to substrate / activation of protein kinase C activity / nicotinate-nucleotide adenylyltransferase activity / neural crest cell migration involved in autonomic nervous system development / regulation of modification of synaptic structure / positive regulation of microtubule binding / delta-catenin binding / B cell proliferation involved in immune response / positive regulation of extracellular matrix organization / peptidase activator activity / neuroepithelial cell differentiation / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cerebellum morphogenesis / positive regulation of blood vessel branching / fibrinogen complex / B-1 B cell homeostasis / mitochondrial depolarization / peptide cross-linking / negative regulation of ubiquitin-protein transferase activity / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / integrin activation / negative regulation of protein serine/threonine kinase activity / ALK mutants bind TKIs / activated T cell proliferation / cellular response to dopamine / cell-substrate junction assembly / regulation of cell motility / regulation of Cdc42 protein signal transduction / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / myoblast proliferation / biological process involved in interaction with symbiont / regulation of hematopoietic stem cell differentiation / proteoglycan binding / Molecules associated with elastic fibres / syntaxin binding / alpha-beta T cell differentiation / cardiac muscle cell proliferation / regulation of T cell differentiation / regulation of axon extension / MET activates PTK2 signaling / HDR through Single Strand Annealing (SSA) / extracellular matrix structural constituent / Syndecan interactions / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / Fc-gamma receptor signaling pathway involved in phagocytosis / p130Cas linkage to MAPK signaling for integrins / Myogenesis / endodermal cell differentiation / regulation of microtubule polymerization / positive regulation of osteoblast proliferation / RUNX2 regulates osteoblast differentiation / platelet-derived growth factor receptor-beta signaling pathway / negative regulation of cellular senescence / positive regulation of focal adhesion assembly / associative learning / Bergmann glial cell differentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / neuromuscular process controlling balance / regulation of endocytosis / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of BMP signaling pathway / negative regulation of mitotic cell cycle / negative regulation of long-term synaptic potentiation / Non-integrin membrane-ECM interactions / actin monomer binding / basement membrane / ECM proteoglycans / endothelial cell migration / RHO GTPases Activate WASPs and WAVEs / positive regulation of T cell migration / canonical NF-kappaB signal transduction / signal transduction in response to DNA damage / Integrin cell surface interactions / positive regulation of axon extension / negative regulation of double-strand break repair via homologous recombination / regulation of cell adhesion / BMP signaling pathway / mismatch repair / negative regulation of endothelial cell apoptotic process
Similarity search - Function
Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / Fibronectin type II domain ...Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / SH2 domain / SHC Adaptor Protein / Kringle-like fold / Fibronectin type III domain / EGF-like domain signature 1. / SH3 domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase ABL1 / Fibronectin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.48 Å
AuthorsWojcik, J.B. / Koide, A. / Koide, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM090324 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM07281 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA014599 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Allosteric Inhibition of Bcr-Abl Kinase by High Affinity Monobody Inhibitors Directed to the Src Homology 2 (SH2)-Kinase Interface.
Authors: Wojcik, J. / Lamontanara, A.J. / Grabe, G. / Koide, A. / Akin, L. / Gerig, B. / Hantschel, O. / Koide, S.
History
DepositionAug 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Data collection
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase ABL1
B: AS25 monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0893
Polymers23,9962
Non-polymers921
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-11 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.281, 74.928, 39.229
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tyrosine-protein kinase ABL1 / Abelson murine leukemia viral oncogene homolog 1 / Abelson tyrosine-protein kinase 1 / Proto- ...Abelson murine leukemia viral oncogene homolog 1 / Abelson tyrosine-protein kinase 1 / Proto-oncogene c-Abl / p150


Mass: 13715.132 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABL1, ABL, JTK7 / Plasmid: pHFT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00519, non-specific protein-tyrosine kinase
#2: Protein AS25 monobody


Mass: 10281.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHFT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02751*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.83 / Details: 0.1M Imidazole pH 7.83 and 3.5M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97872 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2012
RadiationMonochromator: SI 111 SIDE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.48→74.93 Å / Num. obs: 30102 / % possible obs: 98.2 % / Redundancy: 4.9 % / Rsym value: 0.056 / Net I/σ(I): 29.7
Reflection shellResolution: 1.48→1.52 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 4.3 / % possible all: 95.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
RefinementResolution: 1.48→74.93 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.331 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18965 1516 5 %RANDOM
Rwork0.14447 ---
obs0.14677 28548 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.22 Å2-0 Å2
3---0.52 Å2
Refinement stepCycle: 1 / Resolution: 1.48→74.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 0 6 206 1717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211596
X-RAY DIFFRACTIONr_bond_other_d00.021049
X-RAY DIFFRACTIONr_angle_refined_deg1.2051.9452189
X-RAY DIFFRACTIONr_angle_other_deg0.73432557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8535203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.1522.38867
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87415237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.16159
X-RAY DIFFRACTIONr_chiral_restr0.0920.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211784
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02342
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0931.5977
X-RAY DIFFRACTIONr_mcbond_other1.2111.5394
X-RAY DIFFRACTIONr_mcangle_it4.55421595
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.4563619
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.8154.5588
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.84212645
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.482→1.521 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 95 -
Rwork0.2 1960 -
obs--91.7 %

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